Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.

ABSTRACT: Paired-end sequencing is emerging as a key technique for assessing genome rearrangements and structural variation on a genome-wide scale. This technique is particularly useful for detecting copy-neutral rearrangements, such as inversions and translocations, which are common in cancer and can produce novel fusion genes. We address the question of how much sequencing is required to detect rearrangement breakpoints and to localize them precisely using both theoretical models and simulation. We derive a formula for the probability that a fusion gene exists in a cancer genome given a collection of paired-end sequences from this genome. We use this formula to compute fusion gene probabilities in several breast cancer samples, and we find that we are able to accurately predict fusion genes in the

SUBMITTER: Bashir A 

PROVIDER: S-EPMC2278375 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature